Two hours after the quakes – one with a magnitude of 8.6, the other measuring 8.3 – the centre says “the threat has diminished or is over for most areas”.
The alerts caused panic as people fled buildings and made for high ground.
There have been no immediate reports of damage or casualties.
India and Sri Lanka have also lifted their own tsunami warnings.
The region is regularly hit by earthquakes. The Indian Ocean tsunami of 2004 killed 170,000 people in Aceh alone and some 250,000 around the region.
The US Geological Survey (USGS), which documents quakes worldwide, said the first Aceh quake was centred at a depth of 33 km (20 miles), about 495 km from Banda Aceh, the provincial capital.
It was initially reported as 8.9 magnitude but was later revised down to 8.6 by the USGS. Quake officials said a tsunami had been generated and was heading for the coast of Aceh.
A PTWC alert said that sea level readings indicated a tsunami was generated and that it “may already have been destructive along some coasts,” without specifying where.
A Thai disaster official said a 10cm wave had been recorded on Koh Miang island, off Phang Nga.
Indonesian President Susilo Bambang Yudhoyono had told reporters in the capital, Jakarta, that there had been no tsunami reports so far, “but we remain vigilant”.
“Our warning system is working well, and I have ordered the national relief team to fly immediately to Aceh to ensure the situation is under control and to take any necessary action,” he said.
A few hours later, the PTWC renewed its warning after a major aftershock measuring 8.2 struck 16 km (10 miles) beneath the ocean floor and 615 km from Banda Aceh.
An AFP correspondent in Banda Aceh said the aftershock lasted four minutes.
“People are panicking and running outside their home and from buildings,” he said.
The PTWC issues advisory alerts across the region, which state authorities can use to issue their own emergency procedures. Indonesia straddles the Pacific Ring of Fire, a zone of major seismic activity.
Sutopo, a spokesman for Indonesia’s disaster mitigation agency, said electricity had been cut in Aceh and there were traffic jams to access higher ground.
“Sirens and Koran recitals from mosques are everywhere,” he told Reuters.
Tremors were felt as far away as Singapore, Thailand, Sri Lanka, Malaysia, Bangladesh and India. The French island of Reunion was also on alert.
Along the eastern coast of Africa, Kenya and Tanzania issued their own tsunami warnings.
“There was a tremor felt by all of us working in the building,” said a man called Vincent in Calcutta, India.
“All just ran out of the building and people were asked not to use the elevator. There was a minute of chaos where all started ringing up to their family and asking about their well-being.”
Tsunami warning sirens, set up in many vulnerable areas after the 2004 disaster, were heard in Phuket, Thailand, where correspondents said people were calmly following evacuation routes to safe zones.
Roger Musson, a seismologist from Britain’s Royal Geological Survey, said the quakes were unlike those seen off Indonesia in recent years, where ground had been pushed under the continental plate, “flipping up” the seabed.
“It seems to be a large earthquake within the Indian Plate and the plate has broken in a sort of lateral way,” he said.
“It’s a sort of tearing earthquake, and this is much less likely to cause a tsunami because it’s not displacing large volumes of water.”
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